DNA: Natural Single‐stranded

Abstract

Single‐stranded circular or linear viral genomes have been used as model systems to investigate the mechanisms of DNA replication
and gene expression and for the development of highly versatile cloning vectors. Flexible single‐stranded DNA can form hairpin/secondary
structures by base pairing between regions of intramolecular sequence complementarity. Such structures are readily detected
and appear to play important roles in virus‐associated functions in vivo.

(a) Isometric bacteriophage ØX174 and a schematic representation of the phage icosahedron. A spike made of gene H and gene
G proteins is located in the diagram of the virion at the apex (lightly shaded) and is surrounded by gene F coat proteins
(dark shaded area). (b) Filamentous bacteriophage M13. (c) Circular single‐stranded DNA of phage MAC‐1. Adapted from Kornberg
and Baker and Roberts et al.

Secondary structure of MAC‐1 single‐stranded DNA . DNA sequence ladder from Bdellovibrio bacteriovorus single‐stranded phage MAC‐1 was generated by using either Sequenase Ver. 2 protocol at 37°C (b) or ΔTaq DNA polymerase protocol at 60°C (c). Gel loading order in each case from left to right was GATC (Ranu, ). Arrows on right of (b) indicate full‐stops, with the initial full‐stop indicated by a bold arrow. Schematic representation
shows secondary structures of MAC‐1 ssDNA based on data from the sequence ladder generated using Sequenase Ver. 2 or ΔTaq DNA polymerase. Potential secondary structures that lead to formation of DNA polymerase full‐stops are indicated by arrows
(a).

Figure 4.

Hairpin/secondary structure of single‐stranded DNA sequence in G4 and ØX174. Possible hairpin/secondary structures (I and II) of DNA sequences at the complementary‐strand origin of replication (ori) of phage G4 and the hairpin structure of the sequence recognition site of protein n′ possibly involved in DNA replication
of ØX174 are shown. Numbers indicate nucleotide positions on ØX174 map. Adapted from Baas and Jansz .

Figure 5.

Restriction endonuclease map of MAC‐1 phage DNA (a) and genetic map of ØX174 with function of gene products (b). Arrows indicate
the positions of the three promoters and the direction of transcription. Adapted from Kornberg and Baker . (c) A segment of DNA (and amino acid) sequence of ØX174 showing overlap of genes A, B and K.